GenConText 2008

We suggest the following publications (selection): [b][size=medium][color=990000]Virus Evolution[/color][/size][/b] [b]Villarreal, LP[/b] (2005). Viruses and the Evolution of Life. ACM Press, Washington. [b]Bell, P [/b](2006). Sex and the eukaryotic cell cycle is consistent with a viral ancestry for the eukaryotic nucleus. Journal of Theoretical Biology; doi:10.1016/j.jtbi.2006.05.015 [b]Forterre, P.[/b] (2005). The two ages od the RNA world, and the transition to the DNA world: a story of viruses and cells. Biochimie 87(9-10): 793-803 [b]Forterre, P. [/b](2006). Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of the cellular domain. PNAS 103(10): 3669-74. [b]Villarreal LP, DeFilippis VR.[/b] (2000). A hypothesis for DNA viruses as the origin of eukaryotic replication proteins. J Virol 74: 7079-7084. [b][size=medium][color=990000]Natural Genetic Engineering[/color][/size][/b] [b]HH Kazazian.[/b] 2000. L1 retrotransposons shape the mammalian genome. Science 289, 1152-53. [b]Sonea S, Mathieu LG.[/b] Evolution of the genomic systems of prokaryotes and its momentous consequences. Int Microbiol. 2001 Jun;4(2):67-71. [b]Shapiro, J.A.[/b] (2004). A 21st century view of evolution: genome system architecture, repetitive DNA, and natural genetic engineering. Gene 345: 91-100. [b][size=medium][color=990000]Epigenetic Indexing[/color][/size][/b] [b]Jaenisch R. and A. Bird[/b] (2003). Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nature Genetics 33: 245-254. [b]Jenuwein, T. [/b](2002). An RNA-guided pathway for the epigenome. Science 297, 2215–2218. [b]Hake SB, Allis CD[/b].. Histone H3 variants and their potential role in indexing mammalian genomes: the "H3 barcode hypothesis". Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6428-35. [b]Goldberg AD, Allis CD, Bernstein E. [/b]Epigenetics: a landscape takes shape. Cell. 2007 Feb 23;128(4):635-8. [b]Jirtle, R.L., and Skinner, M.K.[/b] (2007). Environmental epigenomics and disease susceptibility. Nature Reviews Genetics 8: 253-562. [b][size=medium][color=990000]Cell-cell channels and virus movement[/color][/size][/b] [b]Piguet V, Sattentau Q[/b] (2004) Dangerous liaisons at the virological synapse. Journal of Clinical Investigations 114: 605-610 [b]Haupt S, Cowan GH, Ziegler A, Roberts AG, Oparka KJ, Torrance L. [/b](2005) The plant-viral movement proteins traffic in the endocytic recycling pathway. Plant Cell 17: 164-181 [b]Baluska, F; Volkmann, D; Barlow, Peter W. (Eds.)[/b] (2006). Cell-Cell Channels. Springer. [b][size=medium][color=990000]Genome Organization and Evolution[/color][/size][/b] [b]Jablonka, E. and M.J. Lamb[/b] (2006). The evolution of information in the major transitions.Journal of Theoretical Biology 239: 236-246. [b]Mattick, J.S.[/b] (2003). Challenging the dogma: the hidden layer of noncoding RNAs in complex organisms. BioEssays 25: 930-939. [b]Odintsova, M.S. and N.P. Yurina[/b] (2005). Genomics and Evolution of Cellular Organelles. Russian Journal of Genetics 41: 957-967. [b]Ryan, F.P.[/b] (2006). Genomic creativity and natural selection. A modern synthesis. Biological Journal of the Linnean Society 88: 655-672. [b]Ryan Frank[/b] (2007). Viruses as symbionts. Symbiosis 44: 11-21 [b] Shapiro, J.A. [/b](2006).Genome Informatics: The Role of DNA in Cellular Computations. Biological Theory 1(3): 288–301. [b]Shapiro, J.A. and R. Sternberg[/b] (2005). Why repetitive DNA is essential to genome function. Biological Reviews 80: 1-24. [b]Vetsigian, K., C. Woese and N. Goldenfeld[/b] (2006). Collective evolution and the genetic code. Proceedings of the National Academy of Sciences of the USA 103: 10696-10701. [b]Rivera MC, Lake JA.[/b] The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature. 2004 Sep 9;431(7005):152-5. [b]Jablonka E, Lamb M[/b] (2005). Evolution in Four Dimensions. MIT Press. [b]Burke WD, Malik HS, Rich SM, Eickbush TH. [/b](2002). Ancient Lineages of Non-LTR-Retrotransposons in the Primitive Eukaryote Giardia lamblia. Molecular Biology and Evolution 19: 619-630. [b][size=medium][color=990000]General References[/color][/size][/b] [b]Van De Vijver G., L. Van Speybroeck, D. De Waele[/b] (2002). Epigentics: A Challenge for Genetics, Evolution and Development. In: L.v. Speybroeck, G.V.d.Vijver and D.DeWaele (eds). From Epigenesis to Epigenetics. The Genome in Context. Annals of the New York Academy of Sciences 981. This volume contains an excellent introduction (pp. 1-6) and articles by Jablonka & Lamb (pp. 82 – 96) and Shapiro (pp. 111-134).